Tallink and other shipowners have been told they cannot appeal a ruling denying them a refund of what they claimed were excessive fairway dues in Finland.
Tallink and Finnlines said the Finnish Supreme Court did not grant leave to appeal last week.
The owners will now not be refunded more than $100m charged between 2001 and 2004.
TradeWinds has reported that shipping companies were originally awarded refunds in 2015, but this was overruled by the Helsinki court of appeal last August.